Minor improvements to rendering with Sphinx

docs/source/10minutes_asreview.rst

@@ -3,19 +3,16 @@
 
 This tutorial will guide you in running the ASReview software. It
 consists of two parts, 0) `the installation of the ASReview
-software <#0-installing-the-asreview-software>`__ and 1) `a
+software <#installing-the-asreview-software>`__ and 1) `a
 demonstration of the Oracle mode of the ASReview
-software <#1-running-oracle-mode-with-the-ptsd-dataset>`__.
+software <#running-oracle-mode-with-the-ptsd-dataset>`__.
 
-0. Installing the ASReview software
-===================================
+Installing the ASReview software
+--------------------------------
 
 Before installing the ASReview software, you have to set up the Command
 Line Interface and Python.
 
-Opening the Command Line Interface (CLI)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 The ASReview can be run through the Command Line Interface (CLI), also
 known as the bash shell. Command Line Interface allows you to interact
 with your computer directly. The CLI is operated by text inputs
@@ -38,9 +35,6 @@ First, open the CLI on your computer:
 If you want to learn more about CLI, you can read `this
 introduction <https://programminghistorian.org/en/lessons/intro-to-bash#opening-your-shell>`__.
 
-Python 3.6+
-^^^^^^^^^^^
-
 The ASReview software requires Python 3.6+. To check the Python version
 on your computer, type the following command in the CLI and press the
 return button:
@@ -63,8 +57,8 @@ If this is not the case, as in the example above, follow the
 instructions in `the next section <#Anaconda>`__ to install a more
 recent version of Python.
 
-0.1 Install Python
-------------------
+Install Python
+~~~~~~~~~~~~~~
 
 To install a recent version of Python, we recommend to install Anaconda.
 Anaconda offers a user-friendly Python environment. Besides Anaconda,
@@ -102,8 +96,8 @@ CLI returns:
 
     Python 3.7.3
 
-0.2 Install ASReview
---------------------
+Install ASReview
+~~~~~~~~~~~~~~~~
 
 If your Python version is 3.6+, you can start installing the ASReview
 software on your computer. To install the ASReview software, follow the
@@ -129,8 +123,8 @@ If ASReview was installed succesfully, you will get output like:
 
 You are now ready to start your first Automated Systematic Review!
 
-1. Running Oracle mode with the PTSD dataset
-============================================
+Running Oracle mode with the PTSD dataset
+-----------------------------------------
 
 As an example, we use the PTSD dataset. This dataset contains x titles
 and abstract on PTSD. From this dataset, we want to select papers
@@ -147,7 +141,7 @@ start this process, run:
 
 The following will show on your screen:
 
-.. code:: bash
+.. code::
 
 
                 _____ _____            _
@@ -178,8 +172,8 @@ Note that if this is the first time you run the ASReview software,
 loading the embedding matrix can take a couple of minutes. In subsequent
 runs, loading the matrix will only take a few seconds.
 
-1.2 Including and excluding papers beforehand
----------------------------------------------
+Including and excluding papers beforehand
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In case you already know of papers you want to in- or exclude from your
 systematic review in advance, you can indicate this.
@@ -211,9 +205,6 @@ systematic review.
 Here, type for example ``31 90 892 3898 3989 4390``, to indicate the
 papers that you want to be excluded from your systematic review.
 
-Options
-~~~~~~~
-
 Instead of setting up the ASReview software step by step, it is possible
 to run the software and indicate papers you want to in- and exclude all
 in one command:
@@ -222,15 +213,15 @@ in one command:
 
     asreview oracle example_ptsd --prior_included 29 181 379 2001 3928 3929 4547 --prior_excluded 31 90 892 3898 3989 4390 --log_file results.log
 
-1.3 Running the model
----------------------
+Running the model
+~~~~~~~~~~~~~~~~~
 
 The software will attempt to classify the papers in the dataset into two
 categories: papers to be included in, and papers to be excluded from the
 systematic review. To improve its decisions, it will ask for your input
 iteratively.
 
-.. code:: bash
+.. code::
 
 
                     (  )   (   )  )
@@ -250,7 +241,7 @@ At each iteration, the model will present you with a number of abstracts
 to include or exclude the presented abstract in your systematic review.
 Indicate your decision by typing ``1`` (include) or ``0`` (exclude).
 
-.. code:: bash
+.. code::
 
     ----------------------------------
     Distributional Assumptions of Growth Mixture Models: Implications for Overextraction of Latent Trajectory Classes
@@ -342,15 +333,12 @@ the options and the defaults.
       --verbose VERBOSE, -v VERBOSE
                             Verbosity
 
-1.4 Wrapping up the Automated Systematic Review
------------------------------------------------
+Wrapping up the Automated Systematic Review
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The ASReview software will keep presenting abstracts. When you feel like
 you have read enough, you can quit by pressing ``S``.
 
-The results.log file
-~~~~~~~~~~~~~~~~~~~~
-
 The results of your Automated Systematic Review can be found in the
 ``results.log`` file. You can open this file by running
 
@@ -362,7 +350,5 @@ In this file you can find:
 
 -  ``pool_proba``
 
-\*© 2019, ASReview Team, Gerbrich Ferdinands
-
-This tutorial has been created using ``asreview v0.2.1`` and
-``macOS Catalina 10.15``.\*
+*© 2019, ASReview Team, Gerbrich Ferdinands.*
+This tutorial has been created using  ``asreview v0.2.1`` and ``macOS Catalina 10.15``.

docs/source/conf.py

@@ -45,8 +45,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'ASReview'
-copyright = '2019, Methodology and Statistics, Utrecht University'
-author = 'Methodology and Statistics, Utrecht University'
+copyright = '2019, ASReview Core Development Team'
+author = 'ASReview Core Development Team, Utrecht University'
 
 # The short X.Y version
 version = ''

docs/source/index.rst

@@ -98,7 +98,7 @@ https://github.com/msdslab/automated-systematic-review.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Basic
+   :caption: Basics
 
    ASReview <self>
 
@@ -108,7 +108,7 @@ https://github.com/msdslab/automated-systematic-review.
 
    api
 
- .. toctree::
+.. toctree::
    :maxdepth: 2
    :caption: Reference